Fig. 1

Schematic representation of the miRTalk workflow and visualization. a Construction of the miRTalkDB based on the EV-derived miRNA databases including ExoCarta, Vesiclepedia, EVmiRNA, and primary literature, and experimentally verified data on MiTIs from miRTarBase and TarBase. Statistics of the miRTalkDB including the number of EV-derived miRNAs, MiTIs, and functional annotation for EV-derived miRNAs of humans, mice, and rats. b Input data of miRTalk including a scRNA-seq data matrix and corresponding cell type annotation for each cell. Detailed diagram of the miRTalk algorithmic process: for a given sender-receiver pair, the widely expressed miRNAs and highly variable target genes were identified based on expression levels. Based on the potential of producing EVs and the expression of miRNAs in senders as well as the activation of miRNA processing machinery and the expression of target genes in receivers, significant MiTIs with negative or positive regulation were enriched. Output data of miRTalk encompassing an enrichment of EV-derived miRNAs and associated MiTIs between sender and receiver cell types. c Analysis of MiTI-mediated CCC using chord, circle, Sankey, and heatmap visualizations, which illustrate the quantity and score of MiTIs from sender cells to receiver cells. d Visualizations of MiTIs and specificity analysis from sender cell types to receiver cell types, represented by chord, circle, bubble, and heatmap plots. EVBS, extracellular vesicle biogenesis and secretion; RISC, RNA-induced silencing complex; RITAC, RNA-induced transcriptional activation complex